pdb_extract - Tutorial

Tutorial for processing a structure solved by X-ray crystallography

The pdb_extract online tool extracts essential details from each step of your structure determination process in preparation for PDB deposition. Refinement statistics, for the most part, will be extracted from the header of your coordinate file. However, if it does not list specific statistics, the LOG files you provide within pdb_extract should supply these extra values. Such information is essential to include in today's PDB entries.

By providing the necessary files and information, you will receive two files in return: one mmCIF file with coordinate and refinement statistics (pdb_extract_coord_#.cif), and the other contains your structure factors (pdb_extract_sf_#.cif). The two files can be used as input for Validation and deposition to ADIT or ADITBeta.

Step 1: Make sure that the X-ray option is selected at http://pdb-extract.rcsb.org/.

Step 2: Upload your fully refined coordinate file into the box provided.

Step 3: Select the file format (PDB or mmCIF) and program used to refine the coordinates.

Step 4: Click the run button to start pdb_extract.

The next series of forms will capture each essential step of the structure determination method,
including all structure factors and resulting output/LOG files used for structure refinement and
protein phasing. Items marked with an asterisk (*) are required.

Step 5: Begin the extraction!

NEXT: Upload these two mmCIF files to ADIT or ADITBeta for data submission.

Note: if you need help for each entry, click the corresponding help button for the entry.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.